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Article ; Online: Structural Insights to the Pathophysiology of Effector Induced Immunostimulation in

Choudhury, Abhigyan

Recent advances in inflammation & allergy drug discovery

2023 Volume 17, Issue 2, Page(s) 133–144

Abstract: Introduction: The worldwide impact of the foodborne pathogen : Methods: To mitigate such a threat, precise structural and functional description of these effectors is necessary. The same has been addressed in this article using accelerated ... ...

Abstract	Introduction: The worldwide impact of the foodborne pathogen Methods: To mitigate such a threat, precise structural and functional description of these effectors is necessary. The same has been addressed in this article using accelerated biocomputational techniques, beginning with the identification of the functional niche of the effectors and their influence over other proteins. Results: The molecular crystal structures were retrieved, and rigorous molecular docking experiments were conducted among the TLRs and effector proteins in order to examine the interactions. The interactions were thereby evaluated and screened according to their respective strengths using parameters including binding affinity, dissociation constant, hydropathy variation, Conclusion: Normal modal analyses in combination with atomistic molecular dynamics simulations that tend to imitate natural cytosolic environments reveal stable and consistent interactions and realistic conformations among the effector-bound TLR complexes. The findings open up new avenues for the development of targeted therapies against
MeSH term(s)	Humans ; Salmonella typhimurium/metabolism ; Bacterial Proteins/chemistry ; Molecular Docking Simulation ; Toll-Like Receptors/metabolism ; Immunization ; Sepsis
Chemical Substances	Bacterial Proteins ; Toll-Like Receptors
Language	English
Publishing date	2023-05-13
Publishing country	Netherlands
Document type	Journal Article
ISSN	2772-2716
ISSN (online)	2772-2716
DOI	10.2174/2772270817666230515125053
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Immunoinformatics and reverse vaccinology approach in designing a novel highly immunogenic multivalent peptide-based vaccine against the human monkeypox virus.

Choudhury, Abhigyan / Chandra, Anshuman / Dawoud, Turki M / Nafidi, Hiba-Allah / Singh, Nagendra / Bourhia, Mohammed

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1295817

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2023-11-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1295817
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Article ; Online: Taming the Storm in the Heart: Exploring Different Therapeutic Choices Against Myocardial Inflammation in COVID-19.

Choudhury, Abhigyan / Mukherjee, Suprabhat

Recent advances in anti-infective drug discovery

2021 Volume 16, Issue 2, Page(s) 89–93

Abstract: Mechanism of cardiac injury in COVID-19 is a serious problem and plays critical role in mediating the severity of the disease. However, the mechanistic insights of the induction of the inflammatory signal leading to cardiac injury was poorly understood. ... ...

Abstract	Mechanism of cardiac injury in COVID-19 is a serious problem and plays critical role in mediating the severity of the disease. However, the mechanistic insights of the induction of the inflammatory signal leading to cardiac injury was poorly understood. However, few recent studies have indicated the involvement of Toll-Like Receptors (TLRs) as the major 'culprit' behind eliciting the initial signal of 'cytokine storm'. As a result, TLRs are now considered as the therapeutic targets to develop efficacious therapeutics. Herein, we present an overall summary on the mechanistic insight of cardiac injury in COVID-19 patients and the therapeutic promises of TLR-targeted therapies.
MeSH term(s)	COVID-19/drug therapy ; Heart/physiopathology ; Humans ; Inflammation ; Myocarditis/drug therapy ; Myocarditis/virology ; Toll-Like Receptors
Chemical Substances	Toll-Like Receptors
Language	English
Publishing date	2021-12-27
Publishing country	United Arab Emirates
Document type	Journal Article
ISSN	2772-4352
ISSN (online)	2772-4352
DOI	10.2174/2772434416666210616124505
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Article ; Online: Immunoinformatics approaches in developing a novel multi-epitope chimeric vaccine protective against Saprolegnia parasitica.

Choudhury, Abhigyan / Kumar, Pawan / Nafidi, Hiba-Allah / Almaary, Khalid S / Wondmie, Gezahign Fentahun / Kumar, Ajit / Bourhia, Mohammed

Scientific reports

2024 Volume 14, Issue 1, Page(s) 2260

Abstract: Saprolegnia parasitica is responsible for devastating infections in fish and poses a tremendous threat to the global aquaculture industry. Presently, no safe and effective control measures are available, on the contrary, use of banned toxic compounds ... ...

Abstract	Saprolegnia parasitica is responsible for devastating infections in fish and poses a tremendous threat to the global aquaculture industry. Presently, no safe and effective control measures are available, on the contrary, use of banned toxic compounds against the pathogen is affecting humans via biomagnification routes. This pioneering study aims to design an effective multi-epitope multi-target vaccine candidate against S. parasitica by targeting key proteins involved in the infection process. The proteins were analyzed and linear B-cell epitopes, MHC class I, and class II epitopes were predicted. Subsequently, highly antigenic epitopes were selected and fused to a highly immunogenic adjuvant, 50S ribosomal protein L7/L12, to design a multi-epitope chimeric vaccine construct. The structure of the vaccine was generated and validated for its stereochemical quality, physicochemical properties, antigenicity, allergenicity, and virulence traits. Molecular docking analyses demonstrated strong binding interactions between the vaccine and piscine immune receptors (TLR5, MHC I, MHC II). Molecular dynamics simulations and binding energy calculations of the complexes, further, reflected the stability and favorable interactions of the vaccine and predicted its cytosolic stability. Immune simulations predicted robust and consistent kinetics of the immune response elicited by the vaccine. The study posits the vaccine as a promising solution to combat saprolegniasis in the aquaculture industry.
MeSH term(s)	Humans ; Animals ; Saprolegnia ; Molecular Docking Simulation ; Immunoinformatics ; Epitopes, T-Lymphocyte ; Computational Biology ; Vaccines ; Epitopes, B-Lymphocyte ; Vaccines, Subunit
Chemical Substances	Epitopes, T-Lymphocyte ; Vaccines ; Epitopes, B-Lymphocyte ; Vaccines, Subunit
Language	English
Publishing date	2024-01-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-52223-z
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Article ; Online: In silico studies on the comparative characterization of the interactions of SARS-CoV-2 spike glycoprotein with ACE-2 receptor homologs and human TLRs.

Choudhury, Abhigyan / Mukherjee, Suprabhat

Journal of medical virology

2020 Volume 92, Issue 10, Page(s) 2105–2113

Abstract: Coronavirus disease-2019 (COVID-19) outbreak due to novel coronavirus or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has come out as a major threat for mankind in recent times. It is continually taking an enormous toll on ... ...

Abstract	Coronavirus disease-2019 (COVID-19) outbreak due to novel coronavirus or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has come out as a major threat for mankind in recent times. It is continually taking an enormous toll on mankind by means of increasing number of deaths, associated comorbidities, and socioeconomic loss around the globe. Unavailability of chemotherapeutics/vaccine has posed tremendous challenges to scientists and doctors for developing an urgent therapeutic strategy. In this connection, the present in silico study aims to understand the sequence divergence of spike protein (the major infective protein of SARS-CoV-2), its mode of interaction with the angiotensin-converting enzyme-2 receptor (ACE2) receptor of human and related animal hosts/reservoir. Moreover, the involvement of the human Toll-like receptors (TLRs) against the spike protein has also been demonstrated. Our data indicated that the spike glycoprotein of SARS-CoV-2 is phylogenetically close to bat coronavirus and strongly binds with ACE2 receptor protein from both human and bat origin. We have also found that cell surface TLRs, especially TLR4 is most likely to be involved in recognizing molecular patterns from SARS-CoV-2 to induce inflammatory responses. The present study supported the zoonotic origin of SARS-CoV-2 from a bat and also revealed that TLR4 may have a crucial role in the virus-induced inflammatory consequences associated with COVID-19. Therefore, selective targeting of TLR4-spike protein interaction by designing competitive TLR4-antagonists could pave a new way to treat COVID-19. Finally, this study is expected to improve our understanding on the immunobiology of SARS-CoV-2 and could be useful in adopting spike protein, ACE2, or TLR-guided intervention strategy against COVID-19 shortly.
MeSH term(s)	Alphacoronavirus/chemistry ; Alphacoronavirus/classification ; Alphacoronavirus/metabolism ; Alphacoronavirus/pathogenicity ; Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/classification ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; Animals ; Binding Sites ; COVID-19/immunology ; COVID-19/virology ; Chiroptera/immunology ; Chiroptera/virology ; Data Mining ; Eutheria/immunology ; Eutheria/virology ; Host-Pathogen Interactions/genetics ; Host-Pathogen Interactions/immunology ; Humans ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Receptors, Virus/chemistry ; Receptors, Virus/classification ; Receptors, Virus/genetics ; Receptors, Virus/metabolism ; SARS-CoV-2/chemistry ; SARS-CoV-2/metabolism ; SARS-CoV-2/pathogenicity ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/classification ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Thermodynamics ; Toll-Like Receptors/chemistry ; Toll-Like Receptors/classification ; Toll-Like Receptors/genetics ; Toll-Like Receptors/metabolism ; Viverridae/immunology ; Viverridae/virology
Chemical Substances	Receptors, Virus ; Spike Glycoprotein, Coronavirus ; Toll-Like Receptors ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-05-17
Publishing country	United States
Document type	Comparative Study ; Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.25987
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Article ; Online: Chemotherapy vs. Immunotherapy in combating nCOVID19: An update.

Choudhury, Abhigyan / Mukherjee, Gargi / Mukherjee, Suprabhat

Human immunology

2021 Volume 82, Issue 9, Page(s) 649–658

Abstract: The nCOVID-19 pandemic initiated its course of contagion from the city of Wuhan and now it has spread all over the globe. SARS-CoV-2 is the causative virus and the infection as well as its symptoms are distributed across the multi-organ perimeters. ... ...

Abstract	The nCOVID-19 pandemic initiated its course of contagion from the city of Wuhan and now it has spread all over the globe. SARS-CoV-2 is the causative virus and the infection as well as its symptoms are distributed across the multi-organ perimeters. Interactions between the host and virus governs the induction of 'cytokine storm' resulting various immunopathological consequences leading to death. Till now it has caused tens of millions of casualties and yet no credible cure has emerged to vision. This article presents a comprehensive overview on the two most promising remedial approaches that are being attempted for the management, treatment, and plausible cure of nCOVID-19. In this context, chemotherapeutic approach primarily aims to interrupt the interactions between the host and the virus causing inhibition of its entry into the host cell and/or its proliferation and suppressing the inflammatory milieu in the infected patients. On the other side, immunotherapeutic approaches aim to modulate the host immunity by fine tuning the inflammatory signaling cascades to achieve phylaxis from the virus and restoring immune-homeostasis. Considering most of the path-breaking findings, combinatorial therapy involving of chemotherapeutics as well as vaccine could usher to be a hope for all of us to eradicate the crisis.
MeSH term(s)	Antiviral Agents/therapeutic use ; COVID-19/pathology ; COVID-19/prevention & control ; COVID-19/therapy ; COVID-19 Vaccines/therapeutic use ; Drug Therapy/methods ; Humans ; Immunologic Factors/therapeutic use ; Immunotherapy/methods ; SARS-CoV-2/drug effects
Chemical Substances	Antiviral Agents ; COVID-19 Vaccines ; Immunologic Factors
Language	English
Publishing date	2021-05-18
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	801524-7
ISSN	1879-1166 ; 0198-8859
ISSN (online)	1879-1166
ISSN	0198-8859
DOI	10.1016/j.humimm.2021.05.001
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Article ; Online: In silico studies on the comparative characterization of the interactions of SARS‐CoV‐2 spike glycoprotein with ACE‐2 receptor homologs and human TLRs

Choudhury, Abhigyan / Mukherjee, Suprabhat

Journal of Medical Virology

2020 Volume 92, Issue 10, Page(s) 2105–2113

Keywords	Virology ; Infectious Diseases ; covid19
Language	English
Publisher	Wiley
Publishing country	us
Document type	Article ; Online
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.25987
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Article: Designing AbhiSCoVac - A single potential vaccine for all 'corona culprits': Immunoinformatics and immune simulation approaches.

Choudhury, Abhigyan / Sen Gupta, Parth Sarthi / Panda, Saroj Kumar / Rana, Malay Kumar / Mukherjee, Suprabhat

Journal of molecular liquids

2022 Volume 351, Page(s) 118633

Abstract: The coronaviridae family has generated highly virulent viruses, including the ones responsible for three major pandemics in last two decades with SARS in 2002, MERS outbreak in 2012 and the current nCOVID19 crisis that has turned the world breadthless. ... ...

Abstract	The coronaviridae family has generated highly virulent viruses, including the ones responsible for three major pandemics in last two decades with SARS in 2002, MERS outbreak in 2012 and the current nCOVID19 crisis that has turned the world breadthless. Future outbreaks are also a plausible threat to mankind. As computational biologists, we are committed to address the need for a universal vaccine that can deter all these pathogenic viruses in a single shot. Notably, the spike proteins present in all these viruses function as credible PAMPs that are majorly sensed by human TLR4 receptors. Our study aims to recognize the amino acid sequence(s) of the viral spike proteins that are precisely responsible for interaction with human TLR4 and to screen the immunogenic epitopes present in them to develop a multi-epitope multi-target chimeric vaccine against the coronaviruses. Molecular design of the constructed vaccine peptide is qualified in silico; additionally, molecular docking and molecular dynamics simulation studies collectively reveal strong and stable interactions of the vaccine construct with TLRs and MHC receptors.
Language	English
Publishing date	2022-01-31
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1491496-7
ISSN	1873-3166 ; 0167-7322
ISSN (online)	1873-3166
ISSN	0167-7322
DOI	10.1016/j.molliq.2022.118633
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Article ; Online: In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by the intracellular TLRs of humans.

Choudhury, Abhigyan / Das, Nabarun Chandra / Patra, Ritwik / Mukherjee, Suprabhat

Journal of medical virology

2021 Volume 93, Issue 4, Page(s) 2476–2486

Abstract: The coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has already resulted in a huge setback to mankind in terms of millions of deaths, while the unavailability of an appropriate ... ...

Abstract	The coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has already resulted in a huge setback to mankind in terms of millions of deaths, while the unavailability of an appropriate therapeutic strategy has made the scenario much more severe. Toll-like receptors (TLRs) are crucial mediators and regulators of host immunity and the role of human cell surface TLRs in SARS-CoV-2 induced inflammatory pathogenesis has been demonstrated recently. However, the functional significance of the human intracellular TLRs including TLR3, 7, 8, and 9 is yet unclear. Hitherto, the involvement of these intracellular TLRs in inducing pro-inflammatory responses in COVID-19 has been reported but the identity of the interacting viral RNA molecule(s) and the corresponding TLRs have not been explored. This study hopes to rationalize the comparative binding of the major SARS-CoV-2 mRNAs to the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drives these interactions. Our in silico study on the binding of all mRNAs with the intracellular TLRs depicts that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are possible virus-associated molecular patterns that bind to TLR3, TLR9, and TLR7, respectively, and trigger downstream cascade reactions. Intriguingly, binding of the viral mRNAs resulted in variable degrees of conformational changes in the ligand-binding domain of the TLRs ratifying the activation of the downstream inflammatory signaling cascade. Taken together, the current study is the maiden report to describe the role of TLR3, 7, and 9 in COVID-19 immunobiology and these could serve as useful targets for the conception of a therapeutic strategy against the pandemic.
MeSH term(s)	Binding Sites ; COVID-19/immunology ; COVID-19/metabolism ; COVID-19/virology ; Computer Simulation ; Genome, Viral ; Humans ; Molecular Docking Simulation ; Protein Binding ; RNA, Messenger/analysis ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Toll-Like Receptors/chemistry ; Toll-Like Receptors/genetics ; Toll-Like Receptors/metabolism
Chemical Substances	RNA, Messenger ; RNA, Viral ; Toll-Like Receptors
Language	English
Publishing date	2021-01-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26776
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Article: In silico studies on the comparative characterization of the interactions of SARS-CoV-2 spike glycoprotein with ACE-2 receptor homologs and human TLRs

Choudhury, Abhigyan / Mukherjee, Suprabhat

J. med. virol

Abstract	Coronavirus disease-2019 (COVID-19) outbreak due to novel coronavirus or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has come out as a major threat for mankind in recent times. It is continually taking an enormous toll on mankind by means of increasing number of deaths, associated comorbidities, and socioeconomic loss around the globe. Unavailability of chemotherapeutics/vaccine has posed tremendous challenges to scientists and doctors for developing an urgent therapeutic strategy. In this connection, the present in silico study aims to understand the sequence divergence of spike protein (the major infective protein of SARS-CoV-2), its mode of interaction with the angiotensin-converting enzyme-2 receptor (ACE2) receptor of human and related animal hosts/reservoir. Moreover, the involvement of the human Toll-like receptors (TLRs) against the spike protein has also been demonstrated. Our data indicated that the spike glycoprotein of SARS-CoV-2 is phylogenetically close to bat coronavirus and strongly binds with ACE2 receptor protein from both human and bat origin. We have also found that cell surface TLRs, especially TLR4 is most likely to be involved in recognizing molecular patterns from SARS-CoV-2 to induce inflammatory responses. The present study supported the zoonotic origin of SARS-CoV-2 from a bat and also revealed that TLR4 may have a crucial role in the virus-induced inflammatory consequences associated with COVID-19. Therefore, selective targeting of TLR4-spike protein interaction by designing competitive TLR4-antagonists could pave a new way to treat COVID-19. Finally, this study is expected to improve our understanding on the immunobiology of SARS-CoV-2 and could be useful in adopting spike protein, ACE2, or TLR-guided intervention strategy against COVID-19 shortly.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #209797
Database	COVID19

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